Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001426.1 Kokia drynarioides strain JFW-HI SEQ_112930, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 927

Length: 1546
ACGTcount: A:0.27, C:0.13, G:0.11, T:0.50


Found at i:581 original size:22 final size:22

Alignment explanation


    Indices: 558--599  Score: 68
    Period size: 22  Copynumber: 2.0  Consensus size: 22

        548 CCCTCTTAAT

                                  
        558 TTTCTATTA-TTTATTTATTTA
          1 TTTCTATTATTTTATTTATTTA

               *                 
        579 TTTGTATTATTTTATTTATTT
          1 TTTCTATTATTTTATTTATTT

        600 TGGGTATTTA


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  21    8  0.42
  22   11  0.58

ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74


Consensus pattern (22 bp):   
TTTCTATTATTTTATTTATTTA

Found at i:590 original size:9 final size:9

Alignment explanation


    Indices: 564--661  Score: 58
    Period size: 9  Copynumber: 10.7  Consensus size: 9

        554 TAATTTTCTA

                     
        564 TTATTTA-T
          1 TTATTTATT

                     
        572 TTATTTATT
          1 TTATTTATT

                      
        581 TGTA-TTATT
          1 T-TATTTATT

                     
        590 TTATTTATT
          1 TTATTTATT

              ***    
        599 TTGGGTATT
          1 TTATTTATT

             *    *   
        608 TAATTTGTAT
          1 TTATTTAT-T

                      *
        618 TTATTTATGGG
          1 TTATTTAT--T

                     
        629 TT-TTTATT
          1 TTATTTATT

             *        
        637 TCATTTCATT
          1 TTATTT-ATT

             *       
        647 TCATTTATT
          1 TTATTTATT

                  
        656 TTATTT
          1 TTATTT

        662 TCTTTTAGTT


Statistics
Matches: 68,  Mismatches: 15, Indels: 13
        0.71            0.16        0.14

Matches are distributed among these distances:
   8   10  0.15
   9   33  0.49
  10   23  0.34
  11    2  0.03

ACGTcount: A:0.20, C:0.03, G:0.08, T:0.68


Consensus pattern (9 bp):   
TTATTTATT

Found at i:623 original size:24 final size:24

Alignment explanation


    Indices: 567--647  Score: 80
    Period size: 24  Copynumber: 3.5  Consensus size: 24

        557 TTTTCTATTA

                         **         
        567 TTTATTTATTTATTTGTA-TT-AT
          1 TTTATTTATTTATGGGTATTTAAT

                                    
        589 TTTATTTATTT-TGGGTATTTAAT
          1 TTTATTTATTTATGGGTATTTAAT

                                  *  
        612 TTGTATTTATTTATGGGT-TTTTAT
          1 TT-TATTTATTTATGGGTATTTAAT

              *         
        636 TTCATTTCATTT
          1 TTTATTT-ATTT

        648 CATTTATTTT


Statistics
Matches: 50,  Mismatches: 4, Indels: 8
        0.81            0.06        0.13

Matches are distributed among these distances:
  21    4  0.08
  22   13  0.26
  23    8  0.16
  24   20  0.40
  25    5  0.10

ACGTcount: A:0.20, C:0.02, G:0.10, T:0.68


Consensus pattern (24 bp):   
TTTATTTATTTATGGGTATTTAAT
Done.